Short-range Interactions Research Articles

Dynamic behavior of helium bubbles in Fe9Cr1.5W0.4Si F/M steel at elevated temperature

The degradation of mechanical properties caused by transmutation/deuterium-tritium reaction produced helium (He) is directly related to the behavior of He bubbles in nuclear materials. Here, the dynamic behavior of He bubbles was in-situ studied in an annealed Fe9Cr1.5W0.4Si ferrite-martensite (F/M) steel using transmission electron microscopy. The critical temperature at which He bubbles started to appear obvious Brownian motion was ∼1013 K. The mobile spherical bubbles gradually evolved into immobile polyhedral bubbles through migration and coalescence, and the critical size between mobile spherical and immobile polyhedral was ∼4 nm. The macroscopic diffusion coefficients of bubbles at 1023 K were obtained as a function of bubble size by quantifying the bubble motion in the two-dimensional plane. Meanwhile, the motion characteristics of bubbles away from or close to dislocation were compared and analyzed in detail. Due to the attraction of dislocations, the migration path of He bubbles exhibited a similar 1D Brownian motion. This was attributed to the short-range elastic interaction between He bubbles and dislocations. These results provide direct evidence and potential insights for understanding the dynamic behavior of He bubbles in metals.

Correlated flat bands and quantum spin liquid state in a cluster Mott insulator

Flat bands are rare in pristine solids and are unstable against electronic correlations or other types of long-range order. Unlike atomic-scale Hubbard systems or Moiré materials, where electronic correlations are either localized or long-ranged, pristine flat band systems with short-range interactions that do not break symmetry spontaneously are less known and intriguing. These systems could bridge the gap between atomic Mott insulators and Moiré correlated insulators, offering a unique platform to explore their mysterious relation. Using an analytical analysis, further verified by numerical calculations, we show that monolayer Nb3Cl8 is a unique flat band system with short-range interactions. We present clear evidence that it is a cluster Mott insulator, which nicely explains the electronic structure observed in angle-resolved photoemission spectroscopy. We further propose that monolayer Nb3Cl8 may constitute a rare example of molecular quantum spin liquid with flat bands.

Phase-field modeling of dislocation–interstitial interactions

The mechanical behavior of body-centered cubic (BCC) materials can be dramatically affected by the presence of interstitial solute atoms. We present a new phase-field dislocation dynamics formulation to include the diffusion of interstitials. Short-range interactions are accounted for by a concentration-dependent lattice energy, and long-range interactions are accounted for by modifications to the elastic energy. The interstitial diffusion law introduces gradients that require methods for minimizing Gibbs oscillations, which is done via a modified Green’s function. The formulation is general to any solute-solvent system and is applied here to Nb-O as a model system, whose interstitial parameters are obtained from ab initio calculations. The effect of O on the core structures of Nb edge and screw dislocations is calculated. The diffusion of O to form interstitial atmospheres around dislocation cores is simulated, as well as the critical stresses required for dislocations to break away or cross slip from these atmospheres. Future applications of the method to simulate complex interstitial embrittlement mechanisms are discussed.

Ultrafast activation of the double-exchange interaction in antiferromagnetic manganites

In doped manganite systems, strong electronic correlations result in rich phase diagrams where electron delocalization strongly affects the magnetic order. Here, we employ a femtosecond all-optical pump-probe scheme to impulsively photodope the antiferromagnetic parent manganite system CaMnO3 and unveil the formation dynamics of a long-range ferromagnetic state. We resonantly target intense charge transfer electronic transitions in CaMnO3 to photodope the system and probe the subsequent dynamics of both charges and spins using a unique combination of time-resolved terahertz spectroscopy and time-resolved magneto-optical Faraday measurements. We demonstrate that photodoping promotes a long-lived population of delocalized electrons and induces a net magnetization, effectively promoting ferromagnetism resulting from light-induced carrier-mediated short-range double-exchange interactions. The picosecond set time of the magnetization, much longer than the electron timescale, and the presence of an excitation threshold are consistent with the formation of ferromagnetic patches in an antiferromagnetic background.

Weak ferromagnetism in a diamagnetically diluted sublattice of Fe3+ ions in solid solutions Y2 −x Fe1 +xTaO7 (x = 0 –0.2) with pyrochlore-like structure

A series of layered solid solutions Y2-xFe1+xTaO7 (x = 0–0.2) was synthesized and a structural transition (space group R3¯ ↔ space group P3121) was observed at x = 0.1. In Y2−xFe1+xTaO7, which belongs to both structural types, geometrically frustrated 2D sublattices of kagome-type are formed, in which Fe3+ ions are coupled by short-range antiferromagnetic interactions, and the transition to the spin glass state is observed at Tg ∼ 4.3 K. A phenomenon of weak ferromagnetism has been detected, the cause of which is probably a small tilt of the Fe3+ spins due to the Dzyaloshinskii–Moriya antisymmetric superexchange.

Structure and Dynamics of NaCl/KCl/CaCl2-EuCln (n = 2, 3) Molten Salts.

Modern molten salt reactor design and the techniques of electrorefining spent nuclear fuels require a better understanding of the chemical and physical behavior of lanthanide/actinide ions with different oxidation states dissolved in various solvent salts. The molecular structures and dynamics that are driven by the short-range interactions between solute cations and anions and long-range solute and solvent cations are still unclear. In order to study the structural change of solute cations caused by different solvent salts, we performed first-principles molecular dynamics simulations in molten salts and extended X-ray absorption fine structure (EXAFS) measurements for the cooled molten salt samples to identify the local coordination environment of Eu2+ and Eu3+ ions in CaCl2, NaCl, and KCl. The simulations reveal that with the increasing polarizing the outer sphere cations from K+ to Na+ to Ca2+, the coordination number (CN) of Cl- in the first solvation shell increases from 5.6 (Eu2+) and 5.9 (Eu3+) in KCl to 6.9 (Eu2+) and 7.0 (Eu3+) in CaCl2. This coordination change is validated by the EXAFS measurements, in which the CN of Cl- around Eu increases from 5 in KCl to 7 in CaCl2. Our simulation shows that the fewer Cl- ions coordinated to Eu leads to a more rigid first coordination shell with longer lifetime. Furthermore, the diffusivities of Eu2+/Eu3+ are related to the rigidity of their first coordination shell of Cl-: the more rigid the first coordination shell is, the slower the solute cations diffuse.

An Agent-Based Statistical Physics Model for Political Polarization: A Monte Carlo Study.

World-wide, political polarization continues unabated, undermining collective decision-making ability. In this issue, we have examined polarization dynamics using a (mean-field) model borrowed from statistical physics, assuming that each individual interacted with each of the others. We use the model to generate scenarios of polarization trends in time in the USA and explore ways to reduce it, as measured by a polarization index that we propose. Here, we extend our work using a more realistic assumption that individuals interact only with "neighbors" (short-range interactions). We use agent-based Monte Carlo simulations to generate polarization scenarios, considering again three USA political groups: Democrats, Republicans, and Independents. We find that mean-field and Monte Carlo simulation results are quite similar. The model can be applied to other political systems with similar polarization dynamics.

Hypo-Osmotic Stress and Pore-Forming Toxins Adjust the Lipid Order in Sheep Red Blood Cell Membranes.

Lipid ordering in cell membranes has been increasingly recognized as an important factor in establishing and regulating a large variety of biological functions. Multiple investigations into lipid organization focused on assessing ordering from temperature-induced phase transitions, which are often well outside the physiological range. However, particular stresses elicited by environmental factors, such as hypo-osmotic stress or protein insertion into membranes, with respect to changes in lipid status and ordering at constant temperature are insufficiently described. To fill these gaps in our knowledge, we exploited the well-established ability of environmentally sensitive membrane probes to detect intramembrane changes at the molecular level. Our steady state fluorescence spectroscopy experiments focused on assessing changes in optical responses of Laurdan and diphenylhexatriene upon exposure of red blood cells to hypo-osmotic stress and pore-forming toxins at room temperature. We verified our utilized experimental systems by a direct comparison of the results with prior reports on artificial membranes and cholesterol-depleted membranes undergoing temperature changes. The significant changes observed in the lipid order after exposure to hypo-osmotic stress or pore-forming toxins resembled phase transitions of lipids in membranes, which we explained by considering the short-range interactions between membrane components and the hydrophobic mismatch between membrane thickness and inserted proteins. Our results suggest that measurements of optical responses from the membrane probes constitute an appropriate method for assessing the status of lipids and phase transitions in target membranes exposed to mechanical stresses or upon the insertion of transmembrane proteins.

Electrostatic complementarity at the interface drives transient protein-protein interactions

Understanding the mechanisms driving bio-molecules binding and determining the resulting complexes’ stability is fundamental for the prediction of binding regions, which is the starting point for drug-ability and design. Characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions, and the consequent shape complementarity between the interacting molecular surfaces are well established. However, no consensus has yet been reached on the role of electrostatic. Here, we perform extensive analyses on a large dataset of protein complexes for which both experimental binding affinity and pH data were available. Probing the amino acid composition, the disposition of the charges, and the electrostatic potential they generated on the protein molecular surfaces, we found that (i) although different classes of dimers do not present marked differences in the amino acid composition and charges disposition in the binding region, (ii) homodimers with identical binding region show higher electrostatic compatibility with respect to both homodimers with non-identical binding region and heterodimers. Interestingly, (iii) shape and electrostatic complementarity, for patches defined on short-range interactions, behave oppositely when one stratifies the complexes by their binding affinity: complexes with higher binding affinity present high values of shape complementarity (the role of the Lennard-Jones potential predominates) while electrostatic tends to be randomly distributed. Conversely, complexes with low values of binding affinity exploit Coulombic complementarity to acquire specificity, suggesting that electrostatic complementarity may play a greater role in transient (or less stable) complexes. In light of these results, (iv) we provide a novel, fast, and efficient method, based on the 2D Zernike polynomial formalism, to measure electrostatic complementarity without the need of knowing the complex structure. Expanding the electrostatic potential on a basis of 2D orthogonal polynomials, we can discriminate between transient and permanent protein complexes with an AUC of the ROC of sim 0.8. Ultimately, our work helps shedding light on the non-trivial relationship between the hydrophobic and electrostatic contributions in the binding interfaces, thus favoring the development of new predictive methods for binding affinity characterization.

Analyzing the strong influence of the cationic environment on the charge carrier’s jumping in a superionic conductor

In this work the relationship between the structure of a solid ionic material and its ionic dynamics has been studied by impedance spectroscopy, differential scanning calorimetry and molecular dynamics simulation. Nanometric samples of AgI were synthesized to study the cation dynamics when it reaches its superionic behavior. The observed thermal events corresponded to the changes obtained on the dc conductivity behavior. This correspondence was microscopically explained by the ion dynamics revealed in the molecular dynamics simulation. The comprehensive analysis made it possible to confirm the weak short-range interactions between silver cations and iodide anions and exposed that the most mobile cation jumps are constrained by their neighbor cations. This finding explains the Kohlrausch–Williams–Watts β parameter value of 0.9 in the α phase where the AgI becomes a superionic conductor, an aspect that becomes essential to design a superionic conductor by doping ionic conductor materials.

Effect of the Addition of Re on the Microstructure and Phase Composition of Haynes 282: Ab Initio Modelling and Experimental Investigation of Additively Manufactured Specimens.

Interactions in a multicomponent Ni-Cr-Mo-Al-Re model alloy were determined by ab initio calculations in order to investigate the Re doping effect on Haynes 282 alloys. Simulation results provided an understanding of short-range interactions in the alloy and successfully predicted the formation of a Cr and Re-rich phase. The Haynes 282 + 3 wt% Re alloy was manufactured using the additive manufacturing direct metal laser sintering (DMLS) technique, in which the presence of the (Cr17Re6)C6 carbide was confirmed by an XRD study. The results provide useful information about the interactions between Ni, Cr, Mo, Al, and Re as a function of temperature. The designed five-element model can lead to a better understanding of phenomena that occur during the manufacture or heat treatment of modern, complex, multicomponent Ni-based superalloys.

Structure-function coupling increases during interictal spikes in temporal lobe epilepsy: A graph signal processing study

ObjectiveStructure-function coupling remains largely unknown in brain disorders. We studied this coupling during interictal epileptic discharges (IEDs), using graph signal processing in temporal lobe epilepsy (TLE). MethodsWe decomposed IEDs of 17 patients on spatial maps, i.e. network harmonics, extracted from a structural connectome. Harmonics were split in smooth maps (long-range interactions reflecting integration) and coarse maps (short-range interactions reflecting segregation) and were used to reconstruct the part of the signal coupled (Xc) and decoupled (Xd) from the structure, respectively. We analysed how Xc and Xd embed the IED energy over time, at global and regional level. ResultsFor Xc, the energy was smaller than for Xd before the IED onset (p < .001), but became larger around the first IED peak (p < .05, cluster 2, C2). Locally, the ipsilateral mesial regions were significantly coupled to the structure over the whole epoch. The ipsilateral hippocampus increased its coupling during C2 (p < .01). ConclusionsAt whole-brain level, segregation gives way to integrative processes during the IED. Locally, brain regions commonly involved in the TLE epileptogenic network increase their reliance on long-range couplings during IED (C2). SignificanceIn TLE, integration mechanisms prevail during the IED and are localized in the ipsilateral mesial temporal regions.

A Low-Complexity Deep Learning Model for Predicting Targeted Sequencing Depth from Probe Sequence

Targeted sequencing has been widely utilized for genomic molecular diagnostics and the emerging DNA data storage paradigm. However, the probe sequences used to enrich regions of interest have different hybridization kinetic properties, resulting in poor sequencing uniformity and setting limitations for the large-scale application of the technology. Here, a low-complexity deep learning model is proposed for prediction of sequencing depth from probe sequences. To capture the representation of probe and target sequences, we utilized a sequence-encoding model that incorporates k-mer and word embedding techniques, providing a streamlined alternative to the intricate computations involved in biochemical feature analysis. We employed bidirectional long short-term memory (Bi-LSTM) to effectively capture both long-range and short-range interactions within the representation. Furthermore, the attention mechanism was adopted to identify pivotal regions in the sequences that significantly influence sequencing depth. The ratio of the predicted sequencing depth to the actual sequencing depth was in the interval of 1/3—3 as the evaluation metric of model accuracy. The prediction accuracy was 94.3% in the human single-nucleotide polymorphism (SNP) panel and 99.7% in the synthetic DNA information storage sequence (SynDNA) panel. Our model substantially reduced data processing time (from 334 min to 4 min of CPU time in the SNP panel) and model parameters (from 300 k to 70 k) compared with the baseline model.

Microstructural Evolution of Zinc-Ion Species from Aqueous to Hydrated Eutectic Electrolyte for Zn-Ion Batteries.

Despite their intrinsic safety and environmental friendliness, typical aqueous Zn-ion rechargeable batteries have been struggling with poor reversibility and electrochemical stability. Hydrated eutectic electrolytes (HEEs) have been attracting extensive attention due to their appealing features of high designability and superior performances over typical aqueous electrolytes. However, an in-depth understanding of unique microstructure in HEEs and the ensuing superior performances remains obscure, limiting the development of enhanced electrolytes. Herein, we demonstrate a distinct evolution path of Zn-ion species from aqueous to superior hydrated eutectic electrolytes, which experience a special transition state enriched with H-bonds between eutectic molecules. Complementary with the well-studied reorganized solvation structure induced by short-ranged salt-solvent interaction, long-range solvent-solvent interactions arising from the H-bond reorganizes the extended electrolyte microstructure, which in turn influences the cation diffusion mechanisms and interfacial reaction kinetics. Overall, we highlight the importance of ion species microstructural evolution in the rational design of superior aqueous electrolytes.

Magnetic bubbles with alternating chirality in domain walls

In magnetic multilayers with perpendicular anisotropy, the competition of short-range and long-range interactions gives rise to the stability of cylindrical magnetic domains, also known as magnetic bubbles. The presence of Dzyaloshinsky-Moriya interaction induced by asymmetric interfaces between magnetic and nonmagnetic layers may lead to the formation of cylindrical bubble domains with Neel-type domain walls across the whole thickness of the multilayer. Such domain walls produce no contrast in Lorentz TEM under the normal incidence of the electron beam to the film. The latter is often used as an argument for the presence of Dzyaloshinskii-Moriya interaction in the system. Here we show that in magnetic multilayers, the absence of the Lorentz TEM contrast might also have another origin. In particular, in the absence of interfacial Dzyaloshinskii-Moriya interaction and weak interlayer exchange coupling, the magnetic bubbles might have Bloch-type domain walls of alternate chirality in adjacent layers. Such domain walls also do not produce magnetic contrast in Lorentz TEM at normal incidence of the electron beam. We show that, in the absence of interlayer exchange coupling, the magnetic bubble domains with the domain walls of fixed and alternate chirality have nearly identical energies and can coexist in the same range of magnetic fields. Using the geodesic nudged elastic band method, we prove that these states are separated by finite energy barriers. Furthermore, we demonstrate that magnetic multilayers with only dipolar coupling, besides the magnetic bubbles with nontrivial topology in all layers, can accommodate solutions with trivial topology within the internal layers.

Superconducting Transition Temperature of the Bose One-Component Plasma.

We present results of numerically exact simulations of the Bose one-component plasma, i.e., a Bose gas with pairwise Coulomb interactions among particles and a uniform neutralizing background. We compute the superconducting transition temperature for a wide range of densities, in two and three dimensions, for both continuous and lattice versions of the model. The Coulomb potential causes the weakly interacting limit to be approached at high density, but gives rise to no qualitatively different behavior, vis-à-vis the superfluid transition, with respect to short-ranged interactions. Our results are of direct relevance to quantitative studies of bipolaron mechanisms of (high-temperature) superconductivity.

Field dipole interaction and polarization effects in light-sheet optical fluorescence microscopy

Polarization plays a crucial role in understanding the interaction of fluorescent molecules in a light field. We report the study on the effect of a field–dipole interaction under polarization light-sheet fluorescence microscopy using the vectorial theory of light. The molecule is suitably modeled as a radiating electric dipole in a polarized electric field (both linear and random), and the system point spread function (PSF) is determined for different orientations of the dipole (both fixed and random). PSF analysis and contour plots suggest distinct nature of a field distribution in each case, indicating the importance of a field–dipole interaction for high-quality fluorescence imaging. The analysis suggests that the field spreads gradually along the polarization axis at a high numerical aperture (NA) of the objective lens, whereas it is more isotropic and homogeneous at low NA. Moreover, fast changes are not observed at low NA (i.e., far from the central lobe in the field contour plots), suggesting the absence of high-frequency components. However, sidelobes are prominent for linear polarized (along x) light. On the other hand, rapid variations are evident for randomly polarized light, depicting the presence of high spatial frequencies in the system optical transfer function. The other significant observation is the distinct frequency spectrum (both kx and ky) for random and fixed dipoles, indicating the significance of dipole orientation in a light-sheet field. Compared to the point-illumination-based fluorescence microscopy, sheet based polarization technique provides a high signal-to-noise ratio, a uniform field, an order large field of view, and critical information (related to the micro-environment of a dipole and its short-range interactions). The study is expected to facilitate polarization-sensitive investigation of large biological specimens (both fixed and live).

DDMut: predicting effects of mutations on protein stability using deep learning.

Understanding the effects of mutations on protein stability is crucial for variant interpretation and prioritisation, protein engineering, and biotechnology. Despite significant efforts, community assessments of predictive tools have highlighted ongoing limitations, including computational time, low predictive power, and biased predictions towards destabilising mutations. To fill this gap, we developed DDMut, a fast and accurate siamese network to predict changes in Gibbs Free Energy upon single and multiple point mutations, leveraging both forward and hypothetical reverse mutations to account for model anti-symmetry. Deep learning models were built by integrating graph-based representations of the localised 3D environment, with convolutional layers and transformer encoders. This combination better captured the distance patterns between atoms by extracting both short-range and long-range interactions. DDMut achieved Pearson's correlations of up to 0.70 (RMSE: 1.37 kcal/mol) on single point mutations, and 0.70 (RMSE: 1.84 kcal/mol) on double/triple mutants, outperforming most available methods across non-redundant blind test sets. Importantly, DDMut was highly scalable and demonstrated anti-symmetric performance on both destabilising and stabilising mutations. We believe DDMut will be a useful platform to better understand the functional consequences of mutations, and guide rational protein engineering. DDMut is freely available as a web server and API at https://biosig.lab.uq.edu.au/ddmut.

Arrested development and fragmentation in strongly-interacting Floquet systems

We explore how interactions can facilitate classical like dynamics in models with sequentially activated hopping. Specifically, we add local and short range interaction terms to the Hamiltonian and ask for conditions ensuring the evolution acts as a permutation on initial local number Fock states. We show that at certain values of hopping and interactions, determined by a set of Diophantine equations, such evolution can be realized. When only a subset of the Diophantine equations is satisfied the Hilbert space can be fragmented into frozen states, states obeying cellular automata like evolution, and subspaces where evolution mixes Fock states and is associated with eigenstates exhibiting high entanglement entropy and level repulsion.

Liquid Crystal Assembly for Ultra-dissymmetric Circularly Polarized Luminescence and Beyond.

Circularly polarized luminescence (CPL) is attracting much interest because it can carry extensive optical information. CPL shows left- or right-handedness and can be regarded as part of high-level visual perception to supply an extra dimension of information with regard to regular light. A key to meeting the needs for practical applications is to develop the emerging field of ultra-dissymmetric CPL. Chiral liquid crystal (LC) assemblies─otherwise referred to as cholesteric liquid crystals (CLCs)─are essentially organized helical superstructures with a highly ordered one-dimensional orientation, and distinctly superior to regular helical supramolecules. CLCs can achieve a perfect equilibrium of molecular short-range interaction and long-range orientational order, enabling molecule-scale chirality on a helical pitch and observable scale. LC assembly could be an ideal strategy for amplifying chirality, making it accessible to ultra-dissymmetric CPL. Herein, we focused on some basic but important issues regarding CPL: (i) How can CPL be created from chiral dyes? (ii) Is the chirality of luminescent dyes an essential factor for the generation of CPL? That is, can all chiral dyes emit CPL and vice versa? (iii) How can CPL be transferred within intermolecular systems, and what principles of CPL transmission should be followed? Given these queries and our work, in this Perspective we discuss the generation, transmission, and modulation of CPL with chiral LC assembly, aiming to design and build up novel chiroptical materials. Recent applications of CPL-active LC microstructures in three-dimensional displays, circularly polarized lasers, and asymmetric catalysis are also discussed.